The name Mackenzie, or MacCoinnich, as it appears in Gaelic, is generally taken to mean "son of Kenneth", and the original Kenneth, who lived in the thirteenth century, is said to have descended from a younger son of Gilleoin of the Aird. The Mackenzies were, without doubt, of Celtic stock and were not among the clans that originated from Norman ancestors. We know little about the generations immediately following Gilleoin, but in 1267 Kenneth was living at Eilean Donan, a stronghold at the mouth of Loch Duich. He must have been an important vassal, for the Earl of Ross appears to have married Kenneth's aunt and thus strengthened the relationship which already existed between the two families. At the start of the fifteenth century the Earldom of Ross came, through marriage, into the hands of the powerful family of MacDonald, who owned vast property on the west of Scotland and called themselves, at first without the King's authority, Lords of the Isles. In this way the Mackenzies became vassals, not of their kinsmen the Earls of Ross but of the MacDonalds. The Lords of the Isles were so powerful and claimed the allegiance of so many clans that they very soon came into conflict with the King. The earliest of their rebellions took place in 1428 after James I had imprisoned the Lord of the Isles and several chiefs who were attending a Parliament at Inverness. 

Alexander Mackenzie of Kintail was one of the chiefs who attended the Parliament of 1427; but, as he was very young at the time, James I sent him not to prison but to school at Perth, which was then one of the centers of the Court. Alexander seems to have taken advantage of his education, for he was later called "the Upright" and his rule of the clan laid the foundations of its future power. Alexander refused to support his superior, the Lord of the Isles, in his later rebellions and the Mackenzies were prominent in defending the King. As a result the Chief obtained royal charters for his land, the earliest being in 1463. Thirteen years later as the result of another rebellion, the Earldom of Ross was declared forfeit to the Crown, and in the same year Alexander Mackenzie was given charters of land to be held directly from the King. A last revolt by younger members of the MacDonald family, under Alexander of Lochalsh, was finally crushed, the leader captured by the Mackenzies, and the Lordship of the Isles itself was forfeit in 1493. This enabled the Mackenzies to obtain new land without antagonizing powerful neighbors and, what was perhaps more important, to acquire clear legal titles from their own superior, the Crown.

Alexander's son, Kenneth, married a daughter of Lord Lovat, his son, John married a daughter of Grant of Grant, while his son, another Kenneth, married Lady Elizabeth Stewart, daughter of the Earl of Atholl and niece of the Earl of Argyll. The power resulting from these alliances was seen after the Government of the infant Mary Queen of Scots had appointed the Earl of Huntly to be "Lieutenant of the North," while Argyll held a similar position in the west. In 1544 Huntly commanded Mackenzie of Kintail to raise his clan against Clanranald of Moidart and, when he refused, ordered an attach on Mackenzie. But the clans supporting Huntly - Grants, Rosses, and Macintoshes - were not inclined to fall out with Mackenzie and would not attack him. From that time onwards Kintail seems to have been recognized as a separate power in the northwest, independent of the Queen's Lieutenant. In 1602, John Mackenzie of Kintail was appointed a Privy Councillor and in 1609 he was created Lord Mackenzie of Kintail. His independent power and influence in the north had been fully recognized.